Bacteriophages of marine Roseobacter

Abstract

The oceans cover ca. 70% of the Earth’s surface and due to their depth encompass around 300 times the habitable volume of the terrestrial environment. The exact proportion of life on Earth that exists in the oceans is unknown as many ocean species remain undiscovered; in particular this holds true for the viruses that infect marine bacterioplankton. It is currently thought that viruses that infect bacteria, bacteriophages or phages, can numerically exceed their hosts by a factor of ten, however, this abundant and diverse group of organisms is still poorly understood. This is especially true of phages that infect members of the Roseobacter clade. Globally, members of the Roseobacter lineage can comprise up to a quarter of the marine microbial community and often dominate the alga-associated bacterial community. In this study phages capable of infecting species of Roseobacter were isolated and characterised. Two Roseovarius-specific phages, RLP1 and RPP1, were isolated from UK coastal waters; morphological and sequence data identified them as belonging to the N4-like genus of Podoviridae. Comparative genomic analysis of both Roseovarius phages to other N4-like phages such as Escherichia coli phage N4 and Sulfitobacter sp. EE-36 phage EE36Φ1, revealed a number of conserved core genes involved in DNA metabolism, transcription control and virion structure. Comparison of N4-like Roseobacter phages (RLP1, RPP1, EE36Φ1 and Ruegeria pomeroyi DSS-3 phage DSS3Φ2) also revealed a number of peripheral genes which are likely to interact directly with host proteins/machinery specific to the Roseobacter group. Unusually, both RLP1 and RPP1 appeared to only infect host cells when in semi-solid agar matrix, but not in liquid culture. Comparison of the outer surface of agar-embedded and planktonic cells revealed different outer-membrane protein and lipopolysaccharide expression profiles. This suggests that some Roseobacter species (spp.) change components of their bacterial cell surface according to their physiological state: agar-embedded/sessile or planktonic and RLP1 and RPP1 exploit this by binding to (a) receptor(s) only expressed during sessile conditions. A number of prophage-like elements were also induced from three Roseobacter spp. by exposure of growing cultures to the DNA-damaging chemical Mitomycin C. These were identified by electron microscopy as belonging to the Siphoviridae family. The results of this project suggest that within the marine environment there remain many uncharacterised phages with peculiar biochemical properties and a wealth of genomic information